R version 2.15.2 (2012-10-26) -- "Trick or Treat"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: i686-pc-linux-gnu (32-bit)

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Type 'license()' or 'licence()' for distribution details.

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> x <- array(list('No'
+ ,'Treatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'Treatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'Treatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'Treatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'Treatment'
+ ,'Yes'
+ ,'Treatment'
+ ,'No'
+ ,'Treatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'Yes'
+ ,'Treatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'Treatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'Treatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'Treatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'Treatment'
+ ,'Yes'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'Treatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'Treatment'
+ ,'Yes'
+ ,'Treatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'Yes'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'Treatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'Yes'
+ ,'Treatment'
+ ,'No'
+ ,'Treatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'Treatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'Yes'
+ ,'Treatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'Treatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'Yes'
+ ,'Treatment'
+ ,'No'
+ ,'Treatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'Yes'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment'
+ ,'No'
+ ,'NoTreatment')
+ ,dim=c(2
+ ,86)
+ ,dimnames=list(c('correct'
+ ,'T40')
+ ,1:86))
>  y <- array(NA,dim=c(2,86),dimnames=list(c('correct','T40'),1:86))
>  for (i in 1:dim(x)[1])
+  {
+  	for (j in 1:dim(x)[2])
+  	{
+  		y[i,j] <- as.numeric(x[i,j])
+  	}
+  }
There were 50 or more warnings (use warnings() to see the first 50)
> par3 = 'Pearson Chi-Squared'
> par2 = '2'
> par1 = '1'
> main = 'Association Plot'
> library(vcd)
Loading required package: MASS
Loading required package: grid
Loading required package: colorspace
> cat1 <- as.numeric(par1) #
> cat2<- as.numeric(par2) #
> simulate.p.value=FALSE
> if (par3 == 'Exact Pearson Chi-Squared by Simulation') simulate.p.value=TRUE
> x <- t(x)
> (z <- array(unlist(x),dim=c(length(x[,1]),length(x[1,]))))
      [,1]  [,2]         
 [1,] "No"  "Treatment"  
 [2,] "No"  "NoTreatment"
 [3,] "No"  "NoTreatment"
 [4,] "No"  "NoTreatment"
 [5,] "No"  "NoTreatment"
 [6,] "No"  "NoTreatment"
 [7,] "No"  "NoTreatment"
 [8,] "No"  "Treatment"  
 [9,] "No"  "NoTreatment"
[10,] "No"  "NoTreatment"
[11,] "No"  "Treatment"  
[12,] "No"  "NoTreatment"
[13,] "No"  "NoTreatment"
[14,] "No"  "Treatment"  
[15,] "No"  "NoTreatment"
[16,] "No"  "Treatment"  
[17,] "Yes" "Treatment"  
[18,] "No"  "Treatment"  
[19,] "No"  "NoTreatment"
[20,] "Yes" "Treatment"  
[21,] "No"  "NoTreatment"
[22,] "No"  "NoTreatment"
[23,] "No"  "NoTreatment"
[24,] "No"  "NoTreatment"
[25,] "No"  "Treatment"  
[26,] "No"  "NoTreatment"
[27,] "No"  "NoTreatment"
[28,] "No"  "NoTreatment"
[29,] "No"  "NoTreatment"
[30,] "No"  "NoTreatment"
[31,] "No"  "NoTreatment"
[32,] "No"  "NoTreatment"
[33,] "No"  "NoTreatment"
[34,] "No"  "Treatment"  
[35,] "No"  "NoTreatment"
[36,] "No"  "NoTreatment"
[37,] "No"  "Treatment"  
[38,] "No"  "NoTreatment"
[39,] "No"  "NoTreatment"
[40,] "No"  "Treatment"  
[41,] "Yes" "NoTreatment"
[42,] "No"  "NoTreatment"
[43,] "No"  "NoTreatment"
[44,] "No"  "Treatment"  
[45,] "No"  "NoTreatment"
[46,] "No"  "NoTreatment"
[47,] "No"  "NoTreatment"
[48,] "No"  "NoTreatment"
[49,] "No"  "NoTreatment"
[50,] "No"  "NoTreatment"
[51,] "No"  "Treatment"  
[52,] "Yes" "Treatment"  
[53,] "No"  "NoTreatment"
[54,] "Yes" "NoTreatment"
[55,] "No"  "NoTreatment"
[56,] "No"  "Treatment"  
[57,] "No"  "NoTreatment"
[58,] "No"  "NoTreatment"
[59,] "No"  "NoTreatment"
[60,] "Yes" "Treatment"  
[61,] "No"  "Treatment"  
[62,] "No"  "NoTreatment"
[63,] "No"  "NoTreatment"
[64,] "No"  "Treatment"  
[65,] "No"  "NoTreatment"
[66,] "No"  "NoTreatment"
[67,] "Yes" "Treatment"  
[68,] "No"  "NoTreatment"
[69,] "No"  "NoTreatment"
[70,] "No"  "NoTreatment"
[71,] "No"  "NoTreatment"
[72,] "No"  "NoTreatment"
[73,] "No"  "NoTreatment"
[74,] "No"  "NoTreatment"
[75,] "No"  "NoTreatment"
[76,] "No"  "Treatment"  
[77,] "No"  "NoTreatment"
[78,] "No"  "NoTreatment"
[79,] "Yes" "Treatment"  
[80,] "No"  "Treatment"  
[81,] "No"  "NoTreatment"
[82,] "No"  "NoTreatment"
[83,] "No"  "NoTreatment"
[84,] "Yes" "NoTreatment"
[85,] "No"  "NoTreatment"
[86,] "No"  "NoTreatment"
> (table1 <- table(z[,cat1],z[,cat2]))
     
      NoTreatment Treatment
  No           60        17
  Yes           3         6
> (V1<-dimnames(y)[[1]][cat1])
[1] "correct"
> (V2<-dimnames(y)[[1]][cat2])
[1] "T40"
> postscript(file="/var/fisher/rcomp/tmp/1ad3d1356024324.ps",horizontal=F,onefile=F,pagecentre=F,paper="special",width=8.3333333333333,height=5.5555555555556) 
> assoc(ftable(z[,cat1],z[,cat2],row.vars=1,dnn=c(V1,V2)),shade=T)
> dev.off()
null device 
          1 
> 
> #Note: the /var/fisher/rcomp/createtable file can be downloaded at http://www.wessa.net/cretab
> load(file="/var/fisher/rcomp/createtable")
> 
> a<-table.start()
> a<-table.row.start(a)
> a<-table.element(a,'Tabulation of Results',ncol(table1)+1,TRUE)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a,paste(V1,' x ', V2),ncol(table1)+1,TRUE)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a, ' ', 1,TRUE)
> for(nc in 1:ncol(table1)){
+ a<-table.element(a, colnames(table1)[nc], 1, TRUE)
+ }
> a<-table.row.end(a)
> for(nr in 1:nrow(table1) ){
+ a<-table.element(a, rownames(table1)[nr], 1, TRUE)
+ for(nc in 1:ncol(table1) ){
+ a<-table.element(a, table1[nr, nc], 1, FALSE)
+ }
+ a<-table.row.end(a)
+ }
> a<-table.end(a)
> table.save(a,file="/var/fisher/rcomp/tmp/2s26i1356024324.tab") 
> (cst<-chisq.test(table1, simulate.p.value=simulate.p.value) )

	Pearson's Chi-squared test with Yates' continuity correction

data:  table1 
X-squared = 6.0598, df = 1, p-value = 0.01383

Warning message:
In chisq.test(table1, simulate.p.value = simulate.p.value) :
  Chi-squared approximation may be incorrect
> if (par3 == 'McNemar Chi-Squared') {
+ (cst <- mcnemar.test(table1))
+ }
> if (par3 != 'McNemar Chi-Squared') {
+ a<-table.start()
+ a<-table.row.start(a)
+ a<-table.element(a,'Tabulation of Expected Results',ncol(table1)+1,TRUE)
+ a<-table.row.end(a)
+ a<-table.row.start(a)
+ a<-table.element(a,paste(V1,' x ', V2),ncol(table1)+1,TRUE)
+ a<-table.row.end(a)
+ a<-table.row.start(a)
+ a<-table.element(a, ' ', 1,TRUE)
+ for(nc in 1:ncol(table1)){
+ a<-table.element(a, colnames(table1)[nc], 1, TRUE)
+ }
+ a<-table.row.end(a)
+ for(nr in 1:nrow(table1) ){
+ a<-table.element(a, rownames(table1)[nr], 1, TRUE)
+ for(nc in 1:ncol(table1) ){
+ a<-table.element(a, round(cst$expected[nr, nc], digits=2), 1, FALSE)
+ }
+ a<-table.row.end(a)
+ }
+ a<-table.end(a)
+ table.save(a,file="/var/fisher/rcomp/tmp/3xaet1356024324.tab") 
+ }
> a<-table.start()
> a<-table.row.start(a)
> a<-table.element(a,'Statistical Results',2,TRUE)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a, cst$method, 2,TRUE)
> a<-table.row.end(a)
> a<-table.row.start(a)
> a<-table.element(a, 'Chi Square Statistic', 1, TRUE)
> a<-table.element(a, round(cst$statistic, digits=2), 1,FALSE)
> a<-table.row.end(a)
> if(!simulate.p.value){
+ a<-table.row.start(a)
+ a<-table.element(a, 'Degrees of Freedom', 1, TRUE)
+ a<-table.element(a, cst$parameter, 1,FALSE)
+ a<-table.row.end(a)
+ }
> a<-table.row.start(a)
> a<-table.element(a, 'P value', 1, TRUE)
> a<-table.element(a, round(cst$p.value, digits=2), 1,FALSE)
> a<-table.row.end(a)
> a<-table.end(a)
> table.save(a,file="/var/fisher/rcomp/tmp/49pzq1356024324.tab") 
> 
> try(system("convert tmp/1ad3d1356024324.ps tmp/1ad3d1356024324.png",intern=TRUE))
character(0)
> 
> 
> proc.time()
   user  system elapsed 
  1.488   0.342   1.810